Observational and numerical modeling studies are conducted to investigate the coupled circulation between Mirs Bay to the east of Hong Kong and the adjacent shelf sea during an upwelling season. Long- and short-term observations are synthesized to characterize the circulations in the bay-shelf region. A three-dimensional coupled bay-shelf-estuary circulation model was developed with realistic topography and forced with time-dependent wind, tides and lateral fluxes to investigate the processes and physics in the circulation of the coupled bay-shelf regime. Based on the validated model, it was found that a strong northeastward coastal upwelling jet persisted over the shelf with highly variable topography outside the bay, and a strong upslope current occurred where the topography was sharply convex. This upslope current intruded into the bay in the lower layer (>10 m) as a cold-water stream. A horizontal anti-cyclonic circulation formed inside the bay with a seaward outflow in the upper layer (<10 m). Momentum and vorticity analyses showed that a southwestward along-isobath pressure gradient force over the convex isobaths off the bay intensified that bay-ward intrusion. Negative relative vorticity advection from the jet was responsible for this pressure gradient force. The horizontal anti-cyclonic circulation and elevation fluctuation inside the bay were determined by the interaction between the intruding shelf current and the topographic trough inside the bay, and they were also baroclinically modulated by the intrusion of denser shelf waters. Winds over Mirs Bay intensified exchange flow across its entrance, but suppressed the anti-cyclonic circulation inside the bay.